The choice between Seychelles and Mnemba really depends on what you're looking to experience. Mnemba probably offers superior private snorkeling and diving, solitude and service as well as opportunity to experience Zanzibar's great culture and history (by spending some time in Stone Town). Eventhough I have not been there, Seychelles is famous for its beauty but not so much for snorkeling and diving. Andbeyond is offering a 6 for 4 special at this time which is a really good deal for some fantastic camps. You can do 2 nights at NCL, and then three nights each at Klein's and Grumeti and then spend the rest of your time in Zanzibar (Mnemba for four nights and a night in Stone town). This would give you four free nights total and you'll love the experience. Staying at both Klein's and Grumeti increases your chances for seeing the migration as it is highly unpredictable.

In regards to Kenya, Masai Mara should be very safe as it is pretty far away from region of conflicts. However, I would avoid Lamu or some of the other northen camps/national parks at this time.